comparison jbrowse2.py @ 63:ac00dcfb5d1d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976

62:ab0d6782a95f

import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.3"
# version pinned for cloning

                            else:
                                this_genome["genome_firstcontig"] = fl
                    else:
                        try:
                            fl = urllib.request.urlopen(fapath + ".fai").readline()
                        except:
                            fl = None
                        if fl:  # is first row of the text fai so the first contig name
                            this_genome["genome_firstcontig"] = (
                                fl.decode("utf8").strip().split()[0]
                            )

        """
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        hic_path = trackData.get("hic_path", None)
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            uri = data
        else:
            uri = "%s.hic" % trackData["label"]

        mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
        samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
        sampu = list(dict.fromkeys(samp))
        samples = [x.split(".")[0] for x in sampu]
        samples.sort()
        logging.warn(
            "$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
            % (" ".join(cmd), mafss, samp, samples)
        )
        trackDict = {
            "type": "MafTrack",

            str(min_gap),
            xml,
        ]
        subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
        gff3_unrebased.close()
        logging.warn("### blastxml to gff3 cmd = %s" % " ".join(cmd))
        return gff3_unrebased.name

    def add_blastxml(self, data, trackData, blastOpts, **kwargs):
        gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
        if "parent" in blastOpts and blastOpts["parent"] != "None":

            cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
            if blastOpts.get("protein", "false") == "true":
                cmd.append("--protein2dna")
            cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
            subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
            logging.warn("### gff3rebase cmd = %s" % " ".join(cmd))
            gff3_rebased.close()
            # Replace original gff3 file
            shutil.copy(gff3_rebased.name, gff3)
            os.unlink(gff3_rebased.name)
        url = "%s.gff3.gz" % trackData["label"]

            for track_conf in self.tracksToAdd[gnome]:
                tId = track_conf["trackId"]
                track_types[tId] = track_conf["type"]
                style_data = default_data["style"].get(tId, None)
                if not style_data:
                    logging.warn(
                        "### No style data in default data %s for %s"
                        % (default_data, tId)
                    )
                    style_data = {"type": "LinearBasicDisplay"}
                if "displays" in track_conf:

                "useuri": x.attrib["useuri"],
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in ass.findall("metadata/genomes/genome")
        ]
        logging.warn("#!!! genomes=%s" % genomes)
        assref_name = jc.process_genomes(genomes)

        for track in ass.find("tracks"):
            track_conf = {}
            track_conf["trackfiles"] = []

63:ac00dcfb5d1d

import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

JB2VER = "v2.10.3"
# version pinned for cloning

                            else:
                                this_genome["genome_firstcontig"] = fl
                    else:
                        try:
                            fl = urllib.request.urlopen(fapath + ".fai").readline()
                        except Exception:
                            fl = None
                        if fl:  # is first row of the text fai so the first contig name
                            this_genome["genome_firstcontig"] = (
                                fl.decode("utf8").strip().split()[0]
                            )

        """
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            uri = data
        else:
            uri = "%s.hic" % trackData["label"]

        mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
        samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
        sampu = list(dict.fromkeys(samp))
        samples = [x.split(".")[0] for x in sampu]
        samples.sort()
        logging.debug(
            "$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
            % (" ".join(cmd), mafss, samp, samples)
        )
        trackDict = {
            "type": "MafTrack",

            str(min_gap),
            xml,
        ]
        subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
        gff3_unrebased.close()
        logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd))
        return gff3_unrebased.name

    def add_blastxml(self, data, trackData, blastOpts, **kwargs):
        gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
        if "parent" in blastOpts and blastOpts["parent"] != "None":

            cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
            if blastOpts.get("protein", "false") == "true":
                cmd.append("--protein2dna")
            cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
            subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
            logging.debug("### gff3rebase cmd = %s" % " ".join(cmd))
            gff3_rebased.close()
            # Replace original gff3 file
            shutil.copy(gff3_rebased.name, gff3)
            os.unlink(gff3_rebased.name)
        url = "%s.gff3.gz" % trackData["label"]

            for track_conf in self.tracksToAdd[gnome]:
                tId = track_conf["trackId"]
                track_types[tId] = track_conf["type"]
                style_data = default_data["style"].get(tId, None)
                if not style_data:
                    logging.debug(
                        "### No style data in default data %s for %s"
                        % (default_data, tId)
                    )
                    style_data = {"type": "LinearBasicDisplay"}
                if "displays" in track_conf:

                "useuri": x.attrib["useuri"],
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in ass.findall("metadata/genomes/genome")
        ]
        assref_name = jc.process_genomes(genomes)

        for track in ass.find("tracks"):
            track_conf = {}
            track_conf["trackfiles"] = []